+1 on Boss BF-2 Flanger, which sounds great. I think Jason Newsted used that on some Metallica albums.

The Boss HM-3 Hyper Metal pedal sounds excellent on bass, and IMO gives the Bass Muff Pi a real run for its money.

Also, EHX makes a cool pedal called the Stereo Electric Mistress, which has flanger and chorus effects. It is a simple pedal to use, which is a kind way of saying that it doesn't have many customizeable options, but sometimes simple is better. It sounds good on bass, too. Video demo here.

There are several distrotion pedals that you should stay clear of because they absolutely suck out all the bottom end, like the Boss OS-2 (Overdrive/Distortion).